BOSTON — The state’s prison chief resigned Thursday after being asked by Gov. Deval Patrick to step aside due to the commissioner’s handling of an investigation into abuse of a patient at Bridgewater State Hospital.

Commissioner Luis Spencer, who began his career as a corrections officer in 1980 and was in charge of the Department of Correction for three years, offered his resignation on Wednesday and Public Safety Secretary Andrea Cabral accepted on Thursday, describing her confidence in his leadership as “shaken.”

“A strong focus on the effective management of the Department’s critical work is essential to sustaining the progress we’ve made. When issues arise, my confidence that leadership at the Department will deal with them promptly and in accordance with our policies, must be unwavering. Due to recent events, that confidence has been shaken,” Cabral said in a statement released to the News Service.

Patrick and Cabral agreed to seek Spencer’s resignation after the commissioner “slowed down” an internal investigation into the alleged “use of force” in May by a corrections officer against a mental health inmate at Bridgewater State Hospital, according to an administration official with knowledge of the circumstances.

Spencer also failed to follow department protocol and notify the secretary in a timely manner about the incident, the source said. Cabral, in her statement, did not provide details of the alleged assault, but the officer has been placed on leave.

Cabral has ordered that an internal investigation into the incident be completed promptly.

Acting Deputy Commissioner Thomas Dickhaut has been appointed acting commissioner effective immediately until a permanent replacement can be found, the administration said.

Spencer was appointed by Patrick as commissioner in May 2011 after a lengthy career in the corrections system that saw him rise through the ranks from officer to a superintendent at three different facilities before becoming assistant deputy commissioner and then acting commissioner.

In a statement at the time of his appointment, Sandra McCroom, undersecretary for criminal justice in the Patrick administration, said, “Mr. Spencer represents a cohort of up and coming managers and superintendents who have long been loyal team players waiting for the opportunity to put their unique prospective (sic) and management ability to work.”

Spencer offered his resignation the same day Patrick administration officials testified before the Legislature’s Judiciary Committee in favor a bill the governor has filed to reform the delivery of forensic mental health services in Massachusetts and shift a majority of individuals, specifically pre-trial defendants, held at Bridgewater State Hospital to a new Department of Mental Health facility.

Bridgewater State Hospital has been under scrutiny since details emerged about the widespread use of restraints at the hospital and the death of a 23-year-old inmate Joshua Messier, which was ruled a homicide. Patrick suspended or fired several guards and officials in connection with the Messier case, and reprimanded Spencer.